I am trying to generate a matrix of small molecules arranged at locations (x, y, z) on a cube. I already have a Tcl script that can generate the required PDB and PSF files. However, I was wondering if there is a way to merge them into a single PDB and PSF file using Tcl itself. Reproduced below is the script to generate the molecules at the given positions.
set psf adenine.xplor_ext.psf set pdb adenine.pdb set resname ADE set a 3 set b 3 set d 10 # first generate in required pdb and psf files set xend [expr $a / 2] set xstart [expr -1 * $xend] set yend [expr $b / 2] set ystart [expr -1 * $yend] set counter 1 for { set i $xstart } { $i <= $xend } { incr i } { for { set j $ystart } { $j <= $yend } { incr j } { mol load psf $psf mol addfile $pdb type pdb waitfor all set sel [atomselect top "resname $resname"] set com [measure center $sel weight mass] $sel moveby [vecscale -1 $com] set xdist [expr $d * $i] set ydist [expr $d * $j] set transvec [list $xdist $ydist 0] puts $transvec $sel moveby $transvec $sel set segname AD$counter $sel set resid $counter $sel writepsf adenine.$i.$j.psf $sel writepdb adenine.$i.$j.pdb incr counter mol delete all } } exit From VMD, I see that the molecules are merged using a call to CHARMM program (at least that is what I could understand from the TkConsole window). But it works by calling 2 PDB files at a time, and is not necessarily what I am looking for. Any help in this regard would be much appreciated.
